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Fusion gene ID: 34156 |
FusionGeneSummary for SLC22A4_PDLIM4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SLC22A4_PDLIM4 | Fusion gene ID: 34156 | Hgene | Tgene | Gene symbol | SLC22A4 | PDLIM4 | Gene ID | 6583 | 8572 |
| Gene name | solute carrier family 22 member 4 | PDZ and LIM domain 4 | |
| Synonyms | DFNB60|OCTN1 | RIL | |
| Cytomap | 5q31.1 | 5q31.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | solute carrier family 22 member 4ET transporterdeafness, autosomal recessive 60ergothioneine transporterintegral membrane transport proteinorganic cation/carnitine transporter 1solute carrier family 22 (organic cation/ergothioneine transporter), mem | PDZ and LIM domain protein 4LIM domain proteinLIM protein RILenigma homologreversion-induced LIM protein | |
| Modification date | 20180522 | 20180519 | |
| UniProtAcc | Q9H015 | P50479 | |
| Ensembl transtripts involved in fusion gene | ENST00000200652, ENST00000491257, | ENST00000253754, ENST00000379018, ENST00000484620, | |
| Fusion gene scores | * DoF score | 1 X 1 X 1=1 | 3 X 1 X 3=9 |
| # samples | 1 | 3 | |
| ** MAII score | log2(1/1*10)=3.32192809488736 | log2(3/9*10)=1.73696559416621 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SLC22A4 [Title/Abstract] AND PDLIM4 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Tumor suppressor gene involved fusion gene, in-frame but not retained their domain. Tumor suppressor gene involved fusion gene, retained protein feature but frameshift. DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain. | ||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | SLC22A4 | GO:0015697 | quaternary ammonium group transport | 9426230 |
| Hgene | SLC22A4 | GO:0015879 | carnitine transport | 16729965 |
| Tgene | PDLIM4 | GO:0031532 | actin cytoskeleton reorganization | 21636573 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | RV | KIRP | TCGA-BQ-5891-01A | SLC22A4 | chr5 | 131630702 | + | PDLIM4 | chr5 | 131598302 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| In-frame | ENST00000200652 | ENST00000253754 | SLC22A4 | chr5 | 131630702 | + | PDLIM4 | chr5 | 131598302 | + |
| In-frame | ENST00000200652 | ENST00000379018 | SLC22A4 | chr5 | 131630702 | + | PDLIM4 | chr5 | 131598302 | + |
| 5CDS-intron | ENST00000200652 | ENST00000484620 | SLC22A4 | chr5 | 131630702 | + | PDLIM4 | chr5 | 131598302 | + |
| intron-3CDS | ENST00000491257 | ENST00000253754 | SLC22A4 | chr5 | 131630702 | + | PDLIM4 | chr5 | 131598302 | + |
| intron-3CDS | ENST00000491257 | ENST00000379018 | SLC22A4 | chr5 | 131630702 | + | PDLIM4 | chr5 | 131598302 | + |
| intron-intron | ENST00000491257 | ENST00000484620 | SLC22A4 | chr5 | 131630702 | + | PDLIM4 | chr5 | 131598302 | + |
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FusionProtFeatures for SLC22A4_PDLIM4 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SLC22A4 | PDLIM4 |
| Sodium-ion dependent, low affinity carnitinetransporter. Probably transports one sodium ion with one moleculeof carnitine. Also transports organic cations such astetraethylammonium (TEA) without the involvement of sodium.Relative uptake activity ratio of carnitine to TEA is 1.78. A keysubstrate of this transporter seems to be ergothioneine (ET).{ECO:0000269|PubMed:10215651, ECO:0000269|PubMed:15795384}. | Isoform 1: Suppresses SRC activation by recognizing andbinding to active SRC and facilitating PTPN13-mediateddephosphorylation of SRC 'Tyr-419' leading to its inactivation.Inactivated SRC dissociates from this protein allowing theinitiation of a new SRC inactivation cycle (PubMed:19307596).Involved in reorganization of the actin cytoskeleton(PubMed:21636573). In nonmuscle cells, binds to ACTN1 (alpha-actinin-1), increases the affinity of ACTN1 to F-actin(filamentous actin), and promotes formation of actin stressfibers. Involved in regulation of the synaptic AMPA receptortransport in dendritic spines of hippocampal pyramidal neuronsdirecting the receptors toward an insertion at the postsynapticmembrane. Links endosomal surface-internalized GRIA1-containingAMPA receptors to the alpha-actinin/actin cytoskeleton. IncreasesAMPA receptor-mediated excitatory postsynaptic currents in neurons(By similarity). {ECO:0000250|UniProtKB:P36202,ECO:0000269|PubMed:19307596, ECO:0000269|PubMed:21636573}. Isoform 2: Involved in reorganization of the actincytoskeleton and in regulation of cell migration. In response tooxidative stress, binds to NQO1, which stabilizes it and protectsit from ubiquitin-independent degradation by the core 20Sproteasome. Stabilized protein is able to heterodimerize withisoform 1 changing the subcellular location of it fromcytoskeleton and nuclei to cytosol, leading to loss of isoforms 1ability to induce formation of actin stress fibers. Counteractsthe effects produced by isoform 1 on organization of actincytoskeleton and cell motility to fine-tune actin cytoskeletonrearrangement and to attenuate cell migration.{ECO:0000269|PubMed:21636573}. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Hgene | SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 1_20 | 131 | 552 | Topological domain | Cytoplasmic |
| Hgene | SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 21_41 | 131 | 552 | Transmembrane | Helical%3B Name%3D1 |
| Tgene | >PDLIM4 | chr5:131630702 | chr5:131598302 | ENST00000253754 | + | 0 | 7 | 253_312 | 31 | 331 | Domain | LIM zinc-binding |
| Tgene | >PDLIM4 | chr5:131630702 | chr5:131598302 | ENST00000379018 | + | 0 | 6 | 253_312 | 31 | 247 | Domain | LIM zinc-binding |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 218_225 | 131 | 552 | Nucleotide binding | ATP |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 163_171 | 131 | 552 | Topological domain | Cytoplasmic |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 193_197 | 131 | 552 | Topological domain | Extracellular |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 219_232 | 131 | 552 | Topological domain | Cytoplasmic |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 254_257 | 131 | 552 | Topological domain | Extracellular |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 279_337 | 131 | 552 | Topological domain | Cytoplasmic |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 359_371 | 131 | 552 | Topological domain | Extracellular |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 393_399 | 131 | 552 | Topological domain | Cytoplasmic |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 421_426 | 131 | 552 | Topological domain | Extracellular |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 42_141 | 131 | 552 | Topological domain | Extracellular |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 448_460 | 131 | 552 | Topological domain | Cytoplasmic |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 482_486 | 131 | 552 | Topological domain | Extracellular |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 508_551 | 131 | 552 | Topological domain | Cytoplasmic |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 142_162 | 131 | 552 | Transmembrane | Helical%3B Name%3D2 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 172_192 | 131 | 552 | Transmembrane | Helical%3B Name%3D3 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 198_218 | 131 | 552 | Transmembrane | Helical%3B Name%3D4 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 233_253 | 131 | 552 | Transmembrane | Helical%3B Name%3D5 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 258_278 | 131 | 552 | Transmembrane | Helical%3B Name%3D6 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 338_358 | 131 | 552 | Transmembrane | Helical%3B Name%3D7 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 372_392 | 131 | 552 | Transmembrane | Helical%3B Name%3D8 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 400_420 | 131 | 552 | Transmembrane | Helical%3B Name%3D9 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 427_447 | 131 | 552 | Transmembrane | Helical%3B Name%3D10 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 461_481 | 131 | 552 | Transmembrane | Helical%3B Name%3D11 |
| Hgene | >SLC22A4 | chr5:131630702 | chr5:131598302 | ENST00000200652 | + | 1 | 10 | 487_507 | 131 | 552 | Transmembrane | Helical%3B Name%3D12 |
| Tgene | PDLIM4 | chr5:131630702 | chr5:131598302 | ENST00000253754 | + | 0 | 7 | 1_84 | 31 | 331 | Domain | PDZ |
| Tgene | PDLIM4 | chr5:131630702 | chr5:131598302 | ENST00000379018 | + | 0 | 6 | 1_84 | 31 | 247 | Domain | PDZ |
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FusionGeneSequence for SLC22A4_PDLIM4 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for SLC22A4_PDLIM4 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| SLC22A4 | PDZK1 | PDLIM4 | RBPMS, ZNF408, EWSR1, KIR3DL2, G3BP1 |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for SLC22A4_PDLIM4 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Hgene | SLC22A4 | Q9H015 | DB00583 | L-Carnitine | Solute carrier family 22 member 4 | small molecule | approved|investigational |
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RelatedDiseases for SLC22A4_PDLIM4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | SLC22A4 | C0010246 | Coxsackievirus Infections | 1 | CTD_human |
| Hgene | SLC22A4 | C0014378 | Enterovirus Infections | 1 | CTD_human |
| Hgene | SLC22A4 | C0027059 | Myocarditis | 1 | CTD_human |
| Tgene | PDLIM4 | C0032460 | Polycystic Ovary Syndrome | 1 | CTD_human |
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